SMTL ID : 7cge.1

The overall structure of nucleotide free MlaFEDB complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-6-mer

Ligands

12 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.1: 10 residues within 4Å: Chain A: H.241, L.244, A.245, G.248, L.249, F.251, V.252 Chain D: L.57 Ligands: PGW.2, PGW.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.245, A:F.251, A:F.251, A:V.252 Salt bridges: A:H.241 PGW.2: 15 residues within 4Å: Chain A: K.15, T.16, F.20, A.23, I.211, T.212, W.215, I.216, F.219, R.237 Chain H: L.15, L.19 Ligands: PGW.1, PGW.3, PGW.7 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: A:A.23, A:I.211, A:T.212, A:W.215, A:I.216, A:F.219, A:F.219, H:L.15, H:L.19 Hydrogen bonds: A:R.237 Salt bridges: A:K.15 PGW.3: 7 residues within 4Å: Chain A: W.195, R.196, V.200, V.207, I.211 Ligands: PGW.2, PGW.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.207, A:I.211 Salt bridges: A:R.196 PGW.4: 19 residues within 4Å: Chain A: Y.81, A.83, M.89, L.90, L.93, S.94, R.97, E.98, L.99 Chain D: V.69, L.70, Q.73, V.77, Y.81 Chain G: L.106, L.107 Chain K: L.107 Chain L: L.106 Ligands: PGW.6 14 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D, 1 interactions with chain G, 2 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: A:Y.81, A:A.83, A:E.98, A:L.99, D:V.69, D:L.70, D:V.77, D:Y.81, D:Y.81, G:L.107, K:L.107, K:L.107, L:L.106 Salt bridges: A:R.97 PGW.5: 6 residues within 4Å: Chain A: Y.49, L.54, L.57 Chain G: W.9 Ligands: PGW.8, PGW.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:L.57, G:W.9, G:W.9 Hydrogen bonds: A:Y.49 PGW.6: 19 residues within 4Å: Chain A: V.69, L.70, Q.73, V.77, Y.81 Chain D: Y.81, A.83, M.89, L.90, L.93, S.94, R.97, E.98, L.99 Chain H: L.107 Chain I: L.106 Chain J: L.106, L.107 Ligands: PGW.4 15 PLIP interactions: 5 interactions with chain D, 2 interactions with chain H, 5 interactions with chain A, 1 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: D:Y.81, D:A.83, D:E.98, D:L.99, H:L.107, H:L.107, A:V.69, A:L.70, A:V.77, A:Y.81, A:Y.81, I:L.106, J:L.106, J:L.107 Salt bridges: D:R.97 PGW.7: 6 residues within 4Å: Chain D: Y.49, L.54, L.57 Chain J: W.9 Ligands: PGW.1, PGW.2 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain D Hydrophobic interactions: J:W.9, J:W.9, D:L.57 Hydrogen bonds: D:Y.49 PGW.8: 10 residues within 4Å: Chain A: L.57 Chain D: H.241, L.244, A.245, G.248, L.249, F.251, V.252 Ligands: PGW.5, PGW.9 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.245, D:F.251, D:F.251, D:V.252 Salt bridges: D:H.241 PGW.9: 15 residues within 4Å: Chain D: K.15, T.16, F.20, A.23, I.211, T.212, W.215, I.216, F.219, R.237 Chain K: L.15, L.19 Ligands: PGW.5, PGW.8, PGW.10 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: D:A.23, D:I.211, D:T.212, D:W.215, D:I.216, D:F.219, D:F.219, K:L.15, K:L.19 Hydrogen bonds: D:R.237 Salt bridges: D:K.15 PGW.10: 7 residues within 4Å: Chain D: W.195, R.196, V.200, V.207, I.211 Ligands: PGW.9, PGW.12 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.207, D:I.211 Salt bridges: D:R.196 PGW.11: 8 residues within 4Å: Chain A: L.157, V.160, W.195, L.203 Chain G: C.25, R.55, R.67 Ligands: PGW.3 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:L.157, A:V.160, A:W.195, A:L.203, A:L.203 Salt bridges: G:R.55 PGW.12: 8 residues within 4Å: Chain D: L.157, V.160, W.195, L.203 Chain J: C.25, R.55, R.67 Ligands: PGW.10 6 PLIP interactions: 1 interactions with chain J, 5 interactions with chain D Salt bridges: J:R.55 Hydrophobic interactions: D:L.157, D:V.160, D:W.195, D:L.203, D:L.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chi, X. et al., Structural mechanism of phospholipids translocation by MlaFEDB complex. Cell Res. (2020)

Release Date

2020-09-09

Peptides

Lipid asymmetry maintenance ABC transporter permease subunit MlaE: AD
Phospholipid ABC transporter ATP-binding protein MlaF: BE
Lipid asymmetry maintenance protein MlaB: CF
Outer membrane lipid asymmetry maintenance protein MlaD: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Membrane

We predict this structure to be a membrane protein.
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Lipid asymmetry maintenance ABC transporter permease subunit MlaE

Phospholipid ABC transporter ATP-binding protein MlaF

Lipid asymmetry maintenance protein MlaB

Outer membrane lipid asymmetry maintenance protein MlaD

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